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Boutet G, Lavaud C, Lesné A, Miteul H, Pilet-Nayel ML, Andrivon D, Lejeune-Hénaut I, Baranger A. Five Regions of the Pea Genome Co-Control Partial Resistance to D. pinodes, Tolerance to Frost, and Some Architectural or Phenological Traits. Genes (Basel) 2023; 14:1399. [PMID: 37510304 PMCID: PMC10379203 DOI: 10.3390/genes14071399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Evidence for reciprocal links between plant responses to biotic or abiotic stresses and architectural and developmental traits has been raised using approaches based on epidemiology, physiology, or genetics. Winter pea has been selected for years for many agronomic traits contributing to yield, taking into account architectural or phenological traits such as height or flowering date. It remains nevertheless particularly susceptible to biotic and abiotic stresses, among which Didymella pinodes and frost are leading examples. The purpose of this study was to identify and resize QTL localizations that control partial resistance to D. pinodes, tolerance to frost, and architectural or phenological traits on pea dense genetic maps, considering how QTL colocalizations may impact future winter pea breeding. QTL analysis revealed five metaQTLs distributed over three linkage groups contributing to both D. pinodes disease severity and frost tolerance. At these loci, the haplotypes of alleles increasing both partial resistance to D. pinodes and frost tolerance also delayed the flowering date, increased the number of branches, and/or decreased the stipule length. These results question both the underlying mechanisms of the joint control of biotic stress resistance, abiotic stress tolerance, and plant architecture and phenology and the methods of marker-assisted selection optimizing stress control and productivity in winter pea breeding.
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Affiliation(s)
- Gilles Boutet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Clément Lavaud
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Henri Miteul
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | | | - Didier Andrivon
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Isabelle Lejeune-Hénaut
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France
| | - Alain Baranger
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
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Wang F, Li S, Kong F, Lin X, Lu S. Altered regulation of flowering expands growth ranges and maximizes yields in major crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1094411. [PMID: 36743503 PMCID: PMC9892950 DOI: 10.3389/fpls.2023.1094411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/04/2023] [Indexed: 06/14/2023]
Abstract
Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.
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Affiliation(s)
| | | | | | - Xiaoya Lin
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
| | - Sijia Lu
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
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3
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Sari H, Eker T, Tosun HS, Mutlu N, Celik I, Toker C. Mapping QTLs for Super-Earliness and Agro-Morphological Traits in RILs Population Derived from Interspecific Crosses between Pisum sativum × P. fulvum. Curr Issues Mol Biol 2023; 45:663-676. [PMID: 36661530 PMCID: PMC9857310 DOI: 10.3390/cimb45010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Earliness in crop plants has a vital role in prevention of heat-induced drought stress and in combating global warming, which is predicted to exacerbate in the near future. Furthermore, earliness may expand production into northern areas or higher altitudes, having relatively shorter growing season and may also expand arable lands to meet global food demands. The primary objective of the present study was to investigate quantitative trait loci (QTLs) for super-earliness and important agro-morphological traits in a recombinant inbred line (RIL) population derived from an interspecific cross. A population of 114 RILs developed through single-seed descent from an interspecific cross involving Pisum sativum L. and P. fulvum Sibth. et Sm. was evaluated to identify QTLs for super-earliness and important agro-morphological traits. A genetic map was constructed with 44 SSRs markers representing seven chromosomes with a total length of 262.6 cM. Of the 14 QTLs identified, two were for super-earliness on LG2, one for plant height on LG3, six for number of pods per plant on LG2, LG4, LG5 and LG6, one for number of seeds per pod on LG6, one for pod length on LG4 and three for harvest index on LG3, LG5, and LG6. AA205 and AA372-1 flanking markers for super-earliness QTLs were suggested for marker-assisted selection (MAS) in pea breeding programs due to high heritability of the trait. This is the first study to map QTLs originating from P. sativum and P. fulvum recently identified species with super-earliness character and the markers (AA205 and AA372-1) linked to QTLs were valuable molecular tools for pea breeding.
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Affiliation(s)
- Hatice Sari
- Faculty of Agriculture, Department of Field Crops, Akdeniz University, Antalya 07070, Turkey
- Department of Crop and Soil Science, Washington State University, Pullman, WA 99164, USA
- Correspondence: (H.S.); (C.T.)
| | - Tuba Eker
- Faculty of Agriculture, Department of Field Crops, Akdeniz University, Antalya 07070, Turkey
| | - Hilal Sule Tosun
- Faculty of Agriculture, Department of Plant Protection, Akdeniz University, Antalya 07070, Turkey
| | - Nedim Mutlu
- Faculty of Agriculture, Department of Ag-Biotech, Akdeniz University, Antalya 07070, Turkey
| | - Ibrahim Celik
- Department of Agricultural and Livestock Production, Pamukkale University, Denizli 20700, Turkey
| | - Cengiz Toker
- Faculty of Agriculture, Department of Field Crops, Akdeniz University, Antalya 07070, Turkey
- Correspondence: (H.S.); (C.T.)
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4
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Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Carrillo-Perdomo E, Magnin-Robert JB, Raffiot B, Deulvot C, Floriot M, Lejeune-Hénaut I, Marget P, Burstin J, Tayeh N, Aubert G. A QTL approach in faba bean highlights the conservation of genetic control of frost tolerance among legume species. FRONTIERS IN PLANT SCIENCE 2022; 13:970865. [PMID: 36340396 PMCID: PMC9627038 DOI: 10.3389/fpls.2022.970865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Frost is a major abiotic stress of winter type faba beans (Vica faba L.) and has adverse effects on crop yield. Climate change, far from reducing the incidence of frost events, is making these phenomena more and more common, severe, and prolonged. Despite the important interaction that the environment has in the tolerance of faba bean to frost, this trait seems to have good levels of heritability. Several QTLs for frost tolerance have already been reported, however, a more robust identification is needed to more precisely identify the genomic regions involved in faba bean tolerance to sub-zero temperatures. Several pea (Pisum sativum L.) and barrel medic (Medicago truncatula L.) frost tolerance QTLs appear to be conserved between these two species, furthering the hypothesis that the genetic control of frost tolerance in legume species might be more generally conserved. In this work, the QTL mapping in two faba bean recombinant inbred line (RIL) populations connected by a common winter-type parent has led to the identification of five genomic regions involved in the control of frost tolerance on linkage groups I, III, IV, and V. Among them, a major and robust QTL of great interest for marker-assisted selection was identified on the lower part of the long-arm of LGI. The synteny between the faba bean frost tolerance QTLs and those previously identified in other legume species such as barrel medic, pea or soybean highlighted at least partial conservation of the genetic control of frost tolerance among different faba bean genetic pools and legume species. Four novel RILs showing high and stable levels of tolerance and the ability to recover from freezing temperatures by accumulating frost tolerance QTLs are now available for breeding programs.
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Affiliation(s)
- Estefanía Carrillo-Perdomo
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
- UMR AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, San Giuliano, France
| | | | - Blandine Raffiot
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
- Terres Inovia, Thiverval-Grignon, France
| | - Chrystel Deulvot
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Isabelle Lejeune-Hénaut
- Département de génétique et protection des cultures, BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, Estrées-Mons, France
| | - Pascal Marget
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
- INRAE, UE115 Domaine Expérimental d’Epoisses, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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6
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Zhao H, Pandey BR, Khansefid M, Khahrood HV, Sudheesh S, Joshi S, Kant S, Kaur S, Rosewarne GM. Combining NDVI and Bacterial Blight Score to Predict Grain Yield in Field Pea. FRONTIERS IN PLANT SCIENCE 2022; 13:923381. [PMID: 35837454 PMCID: PMC9274273 DOI: 10.3389/fpls.2022.923381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Field pea is the most commonly grown temperate pulse crop, with close to 15 million tons produced globally in 2020. Varieties improved through breeding are important to ensure ongoing improvements in yield and disease resistance. Genomic selection (GS) is a modern breeding approach that could substantially improve the rate of genetic gain for grain yield, and its deployment depends on the prediction accuracy (PA) that can be achieved. In our study, four yield trials representing breeding lines' advancement stages of the breeding program (S0, S1, S2, and S3) were assessed with grain yield, aerial high-throughput phenotyping (normalized difference vegetation index, NDVI), and bacterial blight disease scores (BBSC). Low-to-moderate broad-sense heritability (0.31-0.71) and narrow-sense heritability (0.13-0.71) were observed, as the estimated additive and non-additive genetic components for the three traits varied with the different models fitted. The genetic correlations among the three traits were high, particularly in the S0-S2 stages. NDVI and BBSC were combined to investigate the PA for grain yield by univariate and multivariate GS models, and multivariate models showed higher PA than univariate models in both cross-validation and forward prediction methods. A 6-50% improvement in PA was achieved when multivariate models were deployed. The highest PA was indicated in the forward prediction scenario when the training population consisted of early generation breeding stages with the multivariate models. Both NDVI and BBSC are commonly used traits that could be measured in the early growth stage; however, our study suggested that NDVI is a more useful trait to predict grain yield with high accuracy in the field pea breeding program, especially in diseased trials, through its incorporation into multivariate models.
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Affiliation(s)
- Huanhuan Zhao
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Babu R. Pandey
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Majid Khansefid
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Hossein V. Khahrood
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Shimna Sudheesh
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Garry M. Rosewarne
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Melbourne, VIC, Australia
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Mazurier M, Drouaud J, Bahrman N, Rau A, Lejeune-Hénaut I, Delbreil B, Legrand S. Integrated sRNA-seq and RNA-seq Analyses Reveal a microRNA Regulation Network Involved in Cold Response in Pisum sativum L. Genes (Basel) 2022; 13:1119. [PMID: 35885902 PMCID: PMC9322779 DOI: 10.3390/genes13071119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
(1) Background: Cold stress affects growth and development in plants and is a major environmental factor that decreases productivity. Over the past two decades, the advent of next generation sequencing (NGS) technologies has opened new opportunities to understand the molecular bases of stress resistance by enabling the detection of weakly expressed transcripts and the identification of regulatory RNAs of gene expression, including microRNAs (miRNAs). (2) Methods: In this study, we performed time series sRNA and mRNA sequencing experiments on two pea (Pisum sativum L., Ps) lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition. (3) Results: An integrative analysis led to the identification of 136 miRNAs and a regulation network composed of 39 miRNA/mRNA target pairs with discordant expression patterns. (4) Conclusions: Our findings indicate that the cold response in pea involves 11 miRNA families as well as their target genes related to antioxidative and multi-stress defense mechanisms and cell wall biosynthesis.
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Affiliation(s)
- Mélanie Mazurier
- BioEcoAgro Joint Research Unit, Université de Lille, INRAE, Université de Liège, Université de Picardie Jules Verne, 59000 Lille, France; (M.M.); (N.B.); (B.D.)
| | - Jan Drouaud
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
| | - Nasser Bahrman
- BioEcoAgro Joint Research Unit, Université de Lille, INRAE, Université de Liège, Université de Picardie Jules Verne, 59000 Lille, France; (M.M.); (N.B.); (B.D.)
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
| | - Andrea Rau
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350 Jouy-en-Josas, France
| | - Isabelle Lejeune-Hénaut
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
| | - Bruno Delbreil
- BioEcoAgro Joint Research Unit, Université de Lille, INRAE, Université de Liège, Université de Picardie Jules Verne, 59000 Lille, France; (M.M.); (N.B.); (B.D.)
| | - Sylvain Legrand
- Univ. Lille, CNRS, UMR 8198—Evo-Eco-Paleo, 59000 Lille, France
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Moutier N, Baranger A, Fall S, Hanocq E, Marget P, Floriot M, Gauffreteau A. Mixing Ability of Intercropped Wheat Varieties: Stability Across Environments and Tester Legume Species. FRONTIERS IN PLANT SCIENCE 2022; 13:877791. [PMID: 35755684 PMCID: PMC9218859 DOI: 10.3389/fpls.2022.877791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Cereal-legume intercrops are developed mainly in low input or organic farming systems because of the overyielding and numerous ecosystem services they provide. For this management, little advice is available for varietal choice and there are almost no specific breeding programs. Our study aimed to evaluate the mixing ability of a panel of bread wheat genotypes in intercropping and to assess the impact of environment and legume tester choice on this ability. We used partial land equivalent ratios (LERs) to assess the mixing ability of a genotype defined as the combination of its ability to maintain its own yield in intercropping (producer effect, LERw) and to let the mixed species produce (associate effect, LERl). Eight wheat genotypes and 5 legume testers (3 pea and 2 faba bean varieties) were grown in sole crop and in all possible binary intercrops in nine contrasting environments. A mixed model was used to evaluate the effects of wheat genotypes, legume testers, environments, and all the interactions among these 3 factors on LERw and LERl. The chosen wheat genotypes presented contrasting mixing ability, either in terms of producer effect (LERw) or associate effect (LERl). A strong negative correlation was observed between these two components of genotype mixing ability, with an increase in producer effect being generally associated with similar decrease in associate effect, except for three genotypes. The impact of environment on the producer and associate effects was limited and similar between genotypes. Legume tester had a significant effect on both LERw and LERl, making the choice of tester a major issue to reveal the producer or associate effects of wheat genotype. Although the 5 testers showed no significant differences in wheat genotype order for both producer or associate effects, they showed different competitiveness and ability to discriminate genotypes: faba bean was very competitive, resulting in low LERt and low capacity to discriminate wheat genotypes for their mixing ability. On the contrary, pea was less competitive, resulting in higher LERt and better capacity to discriminate wheat genotypes. In particular, the Hr varieties (Geronimo and Spencer) discriminated best the wheat genotypes. Consequences on the implementation of breeding programs for wheat varieties adapted to intercropping are discussed.
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Affiliation(s)
- N. Moutier
- INRAE, Institut Agro Agrocampus Ouest, Université de Rennes 1, UMR 1349 IGEPP, Le Rheu, France
| | - A. Baranger
- INRAE, Institut Agro Agrocampus Ouest, Université de Rennes 1, UMR 1349 IGEPP, Le Rheu, France
| | - S. Fall
- INRAE, Institut Agro Agrocampus Ouest, Université de Rennes 1, UMR 1349 IGEPP, Le Rheu, France
| | - E. Hanocq
- INRAE, UE 0972 GCIE, Estrées-Mons, Péronne, France
| | - P. Marget
- INRAE, UE 115 Epoisses, Bretenière, France
| | | | - A. Gauffreteau
- INRAE, AgroParisTech, Université Paris Saclay, UMR 211 Agronomie, Thiverval-Grignon, France
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9
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Hakeem KR, Alharby HF, Alghamdi KM, Bhat RA. Antioxidant enzyme responses and metabolite functioning of Pisum sativum L. to sewage sludge in arid and semi-arid environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:13201-13210. [PMID: 34585357 DOI: 10.1007/s11356-021-16620-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
The productivity of plants is a direct variant of the countless biotic and abiotic stresses to which a plant is exposed in an environment. This study aimed to investigate the capabilities of leguminous plant garden pea (Pisum sativum L.) to resist water deficit conditions in arid and semi-arid areas when applied with varied doses of sludge for growth response. The effect of sludge doses was evaluated on crop yield, antioxidant enzymes, viz., ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), superoxide dismutase (SOD), and glutathione reductase (GR), and metabolites (ascorbic acid, glutathione, and total protein content). The effective sludge concentrations with respect to seed weight and crop yield were found to be in the following trend: D2 (6.25%)>D3 (12.5%)>D1 (2.5%)>D0 (control) under organic amendment (OA). Conversely, a high dose of the sludge reduced the seed weight and total crop yield. The sludge doses D2 under arid and semi-arid conditions along with organic amendments (OA) significantly enhance the antioxidant enzyme activity, whereas sludge dose D3 with OA ominously regulates the activity of these enzymes. Besides, seeds depicted a considerable increase in ascorbic acid, glutathione, and total protein content in arid and semi-arid conditions upon the application of sludge with OA. Sewage sludge as a source of nutrients indirectly enhances crop yield, antioxidant enzymes, and antioxidant metabolites. Thus, it improves the defense mechanism, reduces abnormal protein glycation, and depletes the susceptibility of protein to proteolysis.
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Affiliation(s)
- Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Hesham F Alharby
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Khalid M Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Rouf Ahmad Bhat
- Division of Environmental Science, Sher-e-Kashmir University of Agricultural Sciences and Technology Kashmir, Srinagar, 190025, India
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10
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Kammoun B, Journet EP, Justes E, Bedoussac L. Cultivar Grain Yield in Durum Wheat-Grain Legume Intercrops Could Be Estimated From Sole Crop Yields and Interspecific Interaction Index. FRONTIERS IN PLANT SCIENCE 2021; 12:733705. [PMID: 34721461 PMCID: PMC8551613 DOI: 10.3389/fpls.2021.733705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/10/2021] [Indexed: 06/12/2023]
Abstract
Ensuring food security for a world population projected to reach over nine billion by 2050 while mitigating the environmental impacts and climate change represent the major agricultural challenges. Diversification of the cropping systems using notably cereal-legume mixtures is one key pathway for such agroecological intensification. Indeed, intercropping is recognised as a practice having the potential to increase and stabilise the yields in comparison with sole crops while limiting the use of inputs notably when species exploit resources in a complementary way. However, predicting intercropped species grain yield remains a challenge because the species respond to competition through complex genotype x cropping mode interactions. Here, we hypothesised that the grain yield achieved by a cultivar in low nitrogen input durum wheat-grain legume intercrops (ICs) could be estimated using a few simple variables. The present work is based on a 2-year field experiment carried out in southwestern France using two durum wheat (Triticum turgidum L.), four winter pea (Pisum sativum L.), and four winter faba bean (Vicia faba L.) genotypes with contrasting characteristics, notably in terms of height and precocity, to explore a wide range of durum wheat-grain legume phenotypes combinations to generate variability in terms of yield and species proportion. The major result is that the yield of durum wheat-grain legume IC component in low nitrogen input conditions could be correctly estimated from only three variables: (i) wheat cultivar full density sole crop (SC) yield, (ii) legume cultivar half density sole crop (SC½) yield, and (iii) an indicator of legume cultivar response to interspecific competition. The latter variable, the interspecific interaction index (IE), reveals cultivars' competitive abilities and tolerance to competition. However, to propose generic IC design and management procedures, further mechanistic understanding is required to better understand the links between tolerance to interspecific competition and cultivar phenotype characteristics. In particular, a special emphasis on the grain legume is needed as their response to interspecific competition appears less predictable than that of durum wheat. Cultivar choice is a key element to optimise the functional complementarity and subsequent IC advantages. This work proposes a simple tool to assist the design of specific breeding programs for cultivars ideotypes adapted to intercropping.
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Affiliation(s)
- Bochra Kammoun
- AGIR, Univ Toulouse, INRAE, Castanet-Tolosan, France
- ARVALIS—Institut du Végétal, Paris, France
| | - Etienne-Pascal Journet
- AGIR, Univ Toulouse, INRAE, Castanet-Tolosan, France
- LIPME, Univ Toulouse, CNRS, Castanet-Tolosan, France
| | - Eric Justes
- AGIR, Univ Toulouse, INRAE, Castanet-Tolosan, France
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11
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Kammoun B, Journet EP, Justes E, Bedoussac L. Cultivar Grain Yield in Durum Wheat-Grain Legume Intercrops Could Be Estimated From Sole Crop Yields and Interspecific Interaction Index. FRONTIERS IN PLANT SCIENCE 2021; 12:733705. [PMID: 34721461 DOI: 10.3389/fpls.2021.233705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/10/2021] [Indexed: 05/27/2023]
Abstract
Ensuring food security for a world population projected to reach over nine billion by 2050 while mitigating the environmental impacts and climate change represent the major agricultural challenges. Diversification of the cropping systems using notably cereal-legume mixtures is one key pathway for such agroecological intensification. Indeed, intercropping is recognised as a practice having the potential to increase and stabilise the yields in comparison with sole crops while limiting the use of inputs notably when species exploit resources in a complementary way. However, predicting intercropped species grain yield remains a challenge because the species respond to competition through complex genotype x cropping mode interactions. Here, we hypothesised that the grain yield achieved by a cultivar in low nitrogen input durum wheat-grain legume intercrops (ICs) could be estimated using a few simple variables. The present work is based on a 2-year field experiment carried out in southwestern France using two durum wheat (Triticum turgidum L.), four winter pea (Pisum sativum L.), and four winter faba bean (Vicia faba L.) genotypes with contrasting characteristics, notably in terms of height and precocity, to explore a wide range of durum wheat-grain legume phenotypes combinations to generate variability in terms of yield and species proportion. The major result is that the yield of durum wheat-grain legume IC component in low nitrogen input conditions could be correctly estimated from only three variables: (i) wheat cultivar full density sole crop (SC) yield, (ii) legume cultivar half density sole crop (SC½) yield, and (iii) an indicator of legume cultivar response to interspecific competition. The latter variable, the interspecific interaction index (IE), reveals cultivars' competitive abilities and tolerance to competition. However, to propose generic IC design and management procedures, further mechanistic understanding is required to better understand the links between tolerance to interspecific competition and cultivar phenotype characteristics. In particular, a special emphasis on the grain legume is needed as their response to interspecific competition appears less predictable than that of durum wheat. Cultivar choice is a key element to optimise the functional complementarity and subsequent IC advantages. This work proposes a simple tool to assist the design of specific breeding programs for cultivars ideotypes adapted to intercropping.
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Affiliation(s)
- Bochra Kammoun
- AGIR, Univ Toulouse, INRAE, Castanet-Tolosan, France
- ARVALIS-Institut du Végétal, Paris, France
| | - Etienne-Pascal Journet
- AGIR, Univ Toulouse, INRAE, Castanet-Tolosan, France
- LIPME, Univ Toulouse, CNRS, Castanet-Tolosan, France
| | - Eric Justes
- AGIR, Univ Toulouse, INRAE, Castanet-Tolosan, France
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12
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Sari H, Sari D, Eker T, Toker C. De novo super-early progeny in interspecific crosses Pisum sativum L. × P. fulvum Sibth. et Sm. Sci Rep 2021; 11:19706. [PMID: 34611237 PMCID: PMC8492716 DOI: 10.1038/s41598-021-99284-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/23/2021] [Indexed: 02/08/2023] Open
Abstract
Earliness in crop plants has a crucial role in avoiding the stress of drought and heat, which are the most important challenging stressors in crop production and are predicted to increase in the near future due to global warming. Furthermore, it provides a guarantee of vegetable production in the short growing season of agricultural lands in the northern hemisphere and at high altitudes. The growing human population needs super early plant cultivars for these agricultural lands to meet future global demands. This study examined de novo super-early progeny, referred to as much earlier than that of the earlier parent, which flowered in 13-17 days and pod setting in 18-29 days after germination, discovered in F2 and studied up to F5 derived from interspecific crosses between garden pea (P. sativum L.) and the most distant relative of pea (P. fulvum Sibth. et Sm.). De novo super-early progeny were found to be earlier by about one month than P. sativum and two months than P. fulvum under short day conditions in the F5 population. In respect of days to flowering and pod setting, de novo super-early progeny had a relatively high level of narrow sense heritability (h2 = 82% and 80%, respectively), indicating that the selections for earliness in segregating populations was effective for improvement of extreme early maturing varieties. De novo super-early progeny could be grown under heat stress conditions due to the escape ability. Vegetable types were not only high yielding but also free of any known undesirable traits from the wild species, such as pod dehiscence and non-uniform maturity. It could be considered complementary to "speed breeding", possibly obtaining more than six generations per year in a suitable climate chamber. Not only de novo super-early progeny but also transgressive segregation for agro-morphological traits can be created via interspecific crosses between P. sativum and P. fulvum, a precious unopened treasure in the second gene pool. Useful progeny obtained from crossing wild species with cultivated species reveal the importance of wild species.
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Affiliation(s)
- Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey.
| | - Duygu Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Tuba Eker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
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13
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Vernoud V, Lebeigle L, Munier J, Marais J, Sanchez M, Pertuit D, Rossin N, Darchy B, Aubert G, Le Signor C, Berdeaux O, Lacaille-Dubois MA, Thompson R. β-Amyrin Synthase1 Controls the Accumulation of the Major Saponins Present in Pea (Pisum sativum). PLANT & CELL PHYSIOLOGY 2021; 62:784-797. [PMID: 33826728 DOI: 10.1093/pcp/pcab049] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The use of pulses as ingredients for the production of food products rich in plant proteins is increasing. However, protein fractions prepared from pea or other pulses contain significant amounts of saponins, glycosylated triterpenes that can impart an undesirable bitter taste when used as an ingredient in foodstuffs. In this article, we describe the identification and characterization of a gene involved in saponin biosynthesis during pea seed development, by screening mutants obtained from two Pisum sativum TILLING (Targeting Induced Local Lesions IN Genomes) populations in two different genetic backgrounds. The mutations studied are located in a gene designated PsBAS1 (β-amyrin synthase1), which is highly expressed in maturing pea seeds and which encodes a protein previously shown to correspond to an active β-amyrin synthase. The first allele is a nonsense mutation, while the second mutation is located in a splice site and gives rise to a mis-spliced transcript encoding a truncated, nonfunctional protein. The homozygous mutant seeds accumulated virtually no saponin without affecting the seed nutritional or physiological quality. Interestingly, BAS1 appears to control saponin accumulation in all other tissues of the plant examined. These lines represent a first step in the development of pea varieties lacking bitterness off-flavors in their seeds. Our work also shows that TILLING populations in different genetic backgrounds represent valuable genetic resources for both crop improvement and functional genomics.
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Affiliation(s)
- Vanessa Vernoud
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - Ludivine Lebeigle
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
- University of Lausanne, Center for Integrative GenomicsLausanne 1015,Switzerland
| | - Jocelyn Munier
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - Julie Marais
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - David Pertuit
- Université de Bourgogne Franche-Comté, Laboratoire de Pharmacognosie EA 4267, Dijon 21079, France
| | - Nadia Rossin
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - Brigitte Darchy
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
| | - Olivier Berdeaux
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon 21000, France
| | | | - Richard Thompson
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon 21000, France
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14
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Annicchiarico P, Nazzicari N, Notario T, Monterrubio Martin C, Romani M, Ferrari B, Pecetti L. Pea Breeding for Intercropping With Cereals: Variation for Competitive Ability and Associated Traits, and Assessment of Phenotypic and Genomic Selection Strategies. FRONTIERS IN PLANT SCIENCE 2021; 12:731949. [PMID: 34630481 PMCID: PMC8495324 DOI: 10.3389/fpls.2021.731949] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/19/2021] [Indexed: 06/12/2023]
Abstract
Mixed stand (MS) cropping of pea with small-grain cereals can produce more productive and environment-friendly grain crops relative to pure stand (PS) crops but may require selection to alleviate the pea competitive disadvantage. This study aimed to assess the pea variation for competitive ability and its associated traits and the efficiency of four phenotypic or genomic selection strategies. A set of 138 semi-leafless, semi-dwarf pea lines belonging to six recombinant inbred line populations and six parent lines were genotyped using genotyping-by-sequencing and grown in PS and in MS simultaneously with one barley and one bread wheat cultivar in two autumn-sown trials in Northern Italy. Cereal companions were selected in a preliminary study that highlighted the paucity of cultivars with sufficient earliness for association. Pea was severely outcompeted in both years albeit with variation for pea proportion ranging from nearly complete suppression (<3%) to values approaching a balanced mixture. Greater pea proportion in MS was associated with greater total yield of the mixture (r ≥ 0.46). The genetic correlation for pea yield across MS and PS conditions slightly exceeded 0.40 in both years. Later onset of flowering and taller plant height at flowering onset displayed a definite correlation with pea yield in MS (r ≥ 0.46) but not in PS, whereas tolerance to ascochyta blight exhibited the opposite pattern. Comparisons of phenotypic selection strategies within or across populations based on predicted or actual yield gains for independent years indicated an efficiency of 52-64% for indirect selection based on pea yield in PS relative to pea yield selection in MS. The efficiency of an indirect selection index including onset of flowering, plant height, and grain yield in PS was comparable to that of pea yield selection in MS. A genome-wide association study based on 5,909 SNP markers revealed the substantial diversity of genomic areas associated with pea yield in MS and PS. Genomic selection for pea yield in MS displayed an efficiency close to that of phenotypic selection for pea yield in MS, and nearly two-fold greater efficiency when also taking into account its shorter selection cycle and smaller evaluation cost.
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15
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Pandey AK, Rubiales D, Wang Y, Fang P, Sun T, Liu N, Xu P. Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:755-776. [PMID: 33433637 DOI: 10.1007/s00122-020-03751-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/10/2020] [Indexed: 05/09/2023]
Abstract
Pea (Pisum sativum L.), a cool-season legume crop grown in more than 85 countries, is the second most important grain legume and one of the major green vegetables in the world. While pea was historically studied as the genetic model leading to the discovery of the laws of genetics, pea research has lagged behind that of other major legumes in the genomics era, due to its large and complex genome. The evolving climate change and growing population have posed grand challenges to the objective of feeding the world, making it essential to invest research efforts to develop multi-omics resources and advanced breeding tools to support fast and continuous development of improved pea varieties. Recently, the pea researchers have achieved key milestones in omics and molecular breeding. The present review provides an overview of the recent important progress including the development of genetic resource databases, high-throughput genotyping assays, reference genome, genes/QTLs responsible for important traits, transcriptomic, proteomic, and phenomic atlases of various tissues under different conditions. These multi-faceted resources have enabled the successful implementation of various markers for monitoring early-generation populations as in marker-assisted backcrossing breeding programs. The emerging new breeding approaches such as CRISPR, speed breeding, and genomic selection are starting to change the paradigm of pea breeding. Collectively, the rich omics resources and omics-enable breeding approaches will enhance genetic gain in pea breeding and accelerate the release of novel pea varieties to meet the elevating demands on productivity and quality.
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Affiliation(s)
- Arun K Pandey
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
| | - Yonggang Wang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Pingping Fang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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16
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Kumar A, Sandhu N, Venkateshwarlu C, Priyadarshi R, Yadav S, Majumder RR, Singh VK. Development of introgression lines in high yielding, semi-dwarf genetic backgrounds to enable improvement of modern rice varieties for tolerance to multiple abiotic stresses free from undesirable linkage drag. Sci Rep 2020; 10:13073. [PMID: 32753648 PMCID: PMC7403580 DOI: 10.1038/s41598-020-70132-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Occurrence of multiple abiotic stresses in a single crop season has become more frequent than before. Most of the traditional donors possessing tolerance to abiotic stresses are tall, low-yielding with poor grain quality. To facilitate efficient use of complex polygenic traits in rice molecular breeding research, we undertook development of introgression lines in background of high-yielding, semi-dwarf varieties with good grain quality. The study reports the development and evaluations of over 25,000 introgression lines in eleven elite rice genetic backgrounds for improvement of yield under multiple abiotic-stresses such as drought, flood, high/low temperature. The developed introgression lines within each genetic background are near isogenic/recombinant inbred lines to their recipient recurrent parent with 50 to 98% background recovery and additionally carry QTLs/genes for abiotic stresses. The multiple-stress tolerant pyramided breeding lines combining high yield under normal situation and good yield under moderate to severe reproductive-stage drought, semi-dwarf plant type with good grain quality traits have been developed. The introgression lines in dwarf backgrounds open new opportunity to improve other varieties without any linkage drag as well as facilitate cloning of QTLs, identification and functional characterization of candidate genes, mechanisms associated with targeted QTLs and the genetic networks underlying complex polygenic traits.
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Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, Metro Manila, Philippines. .,IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, India.
| | - Nitika Sandhu
- International Rice Research Institute, Metro Manila, Philippines.,Punjab Agricultural University, Ludhiana, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Rahul Priyadarshi
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India.,International Rice Research Institute, Guwahati, Assam, India
| | - Shailesh Yadav
- International Rice Research Institute, Metro Manila, Philippines
| | | | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
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17
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Beji S, Fontaine V, Devaux R, Thomas M, Negro SS, Bahrman N, Siol M, Aubert G, Burstin J, Hilbert JL, Delbreil B, Lejeune-Hénaut I. Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea. BMC Genomics 2020; 21:536. [PMID: 32753054 PMCID: PMC7430820 DOI: 10.1186/s12864-020-06928-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative trait loci (QTLs) have previously been detected from bi-parental mapping populations, giving an overview of the genome regions governing this trait. The recent development of high-throughput genotyping tools for pea brings the opportunity to undertake genetic association studies in order to capture a higher allelic diversity within large collections of genetic resources as well as to refine the localization of the causal polymorphisms thanks to the high marker density. In this study, a genome-wide association study (GWAS) was performed using a set of 365 pea accessions. Phenotyping was carried out by scoring frost damages in the field and in controlled conditions. The association mapping collection was also genotyped using an Illumina Infinium® BeadChip, which allowed to collect data for 11,366 single nucleotide polymorphism (SNP) markers. RESULTS GWAS identified 62 SNPs significantly associated with frost tolerance and distributed over six of the seven pea linkage groups (LGs). These results confirmed 3 QTLs that were already mapped in multiple environments on LG III, V and VI with bi-parental populations. They also allowed to identify one locus, on LG II, which has not been detected yet and two loci, on LGs I and VII, which have formerly been detected in only one environment. Fifty candidate genes corresponding to annotated significant SNPs, or SNPs in strong linkage disequilibrium with the formers, were found to underlie the frost damage (FD)-related loci detected by GWAS. Additionally, the analyses allowed to define favorable haplotypes of markers for the FD-related loci and their corresponding accessions within the association mapping collection. CONCLUSIONS This study led to identify FD-related loci as well as corresponding favorable haplotypes of markers and representative pea accessions that might to be used in winter pea breeding programs. Among the candidate genes highlighted at the identified FD-related loci, the results also encourage further attention to the presence of C-repeat Binding Factors (CBF) as potential genetic determinants of the frost tolerance locus on LG VI.
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Affiliation(s)
- Sana Beji
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Véronique Fontaine
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | | | | | - Sandra Silvia Negro
- GQE - Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Nasser Bahrman
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Mathieu Siol
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jean-Louis Hilbert
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Bruno Delbreil
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
| | - Isabelle Lejeune-Hénaut
- BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203 Estrées-Mons, France
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18
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Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses. PLANTS 2019; 8:plants8080288. [PMID: 31443248 PMCID: PMC6724123 DOI: 10.3390/plants8080288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/30/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022]
Abstract
Low temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them.
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19
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Raggi L, Caproni L, Carboni A, Negri V. Genome-Wide Association Study Reveals Candidate Genes for Flowering Time Variation in Common Bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2019; 10:962. [PMID: 31428109 PMCID: PMC6689981 DOI: 10.3389/fpls.2019.00962] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/10/2019] [Indexed: 05/13/2023]
Abstract
The common bean is one of the most important staples in many areas of the world. Extensive phenotypic and genetic characterization of unexplored bean germplasm are still needed to unlock the breeding potential of this crop. Dissecting genetic control of flowering time is of pivotal importance to foster common bean breeding and to develop new varieties able to adapt to changing climatic conditions. Indeed, flowering time strongly affects yield and plant adaptation ability. The aim of this study was to investigate the genetic control of days to flowering using a whole genome association approach on a panel of 192 highly homozygous common bean genotypes purposely developed from landraces using Single Seed Descent. The phenotypic characterization was carried out at two experimental sites throughout two growing seasons, using a randomized partially replicated experimental design. The same plant material was genotyped using double digest Restriction-site Associated DNA sequencing producing, after a strict quality control, a dataset of about 50 k Single Nucleotide Polymorphisms (SNPs). The Genome-Wide Association Study revealed significant and meaningful associations between days to flowering and several SNP markers; seven genes are proposed as the best candidates to explain the detected associations.
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Affiliation(s)
- Lorenzo Raggi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Leonardo Caproni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Andrea Carboni
- CREA Research Centre for Cereal and Industrial Crops, Bologna, Italy
| | - Valeria Negri
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
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Zheng Y, Xu F, Li Q, Wang G, Liu N, Gong Y, Li L, Chen ZH, Xu S. QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing. Front Genet 2018; 9:615. [PMID: 30568674 PMCID: PMC6290080 DOI: 10.3389/fgene.2018.00615] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 11/23/2018] [Indexed: 12/04/2022] Open
Abstract
Leaf shape is an important trait that influences the utilization rate of light, and affects quality and yield of pea (Pisum sativum). In the present study, a joint method of high-density genetic mapping using specific locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was applied to rapidly detect loci with leaf shape traits. A total of 7,146 polymorphic SLAFs containing 12,213 SNP markers were employed to construct a high-density genetic map for pea. We conducted quantitative trait locus (QTL) mapping on an F2 population to identify QTLs associated with leaf shape traits. Moreover, SLAF-BSA was conducted on the same F2 population to identify the single nucleotide polymorphism (SNP) markers linked to leaf shape in pea. Two QTLs (qLeaf_or-1, qLeaf_or-2) were mapped on linkage group 7 (LG7) for pea leaf shape. Through alignment of SLAF markers with Cicer arietinum, Medicago truncatula, and Glycine max, the pea LGs were assigned to their corresponding homologous chromosomal groups. The comparative genetic analysis showed that pea is more closely related to M. truncatula. Based on the sequencing results of two pools with different leaf shape, 179 associated markers were obtained after association analysis. The joint analysis of SLAF-seq and BSA showed that the QTLs obtained from mapping on a high-density genetic map are convincing due to the closely associated map region with the BSA results, which provided more potential markers related to leaf shape. Thus, the identified QTLs could be used in marker-assisted selection for pea breeding in the future. Our study revealed that joint analysis of QTL mapping on a high-density genetic map and BSA-seq is a cost-effective and accurate method to reveal genetic architecture of target traits in plant species without a reference genome.
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Affiliation(s)
- Yuanting Zheng
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Xu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qikai Li
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Gangjun Wang
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Na Liu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaming Gong
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lulu Li
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhong-Hua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Shengchun Xu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Kulaeva OA, Zhernakov AI, Afonin AM, Boikov SS, Sulima AS, Tikhonovich IA, Zhukov VA. Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers. PLoS One 2017; 12:e0186713. [PMID: 29073280 PMCID: PMC5658071 DOI: 10.1371/journal.pone.0186713] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/17/2017] [Indexed: 11/19/2022] Open
Abstract
Pea (Pisum sativum L.) is the oldest model object of plant genetics and one of the most agriculturally important legumes in the world. Since the pea genome has not been sequenced yet, identification of genes responsible for mutant phenotypes or desirable agricultural traits is usually performed via genetic mapping followed by candidate gene search. Such mapping is best carried out using gene-based molecular markers, as it opens the possibility for exploiting genome synteny between pea and its close relative Medicago truncatula Gaertn., possessing sequenced and annotated genome. In the last 5 years, a large number of pea gene-based molecular markers have been designed and mapped owing to the rapid evolution of "next-generation sequencing" technologies. However, the access to the complete set of markers designed worldwide is limited because the data are not uniformed and therefore hard to use. The Pea Marker Database was designed to combine the information about pea markers in a form of user-friendly and practical online tool. Version 1 (PMD1) comprises information about 2484 genic markers, including their locations in linkage groups, the sequences of corresponding pea transcripts and the names of related genes in M. truncatula. Version 2 (PMD2) is an updated version comprising 15944 pea markers in the same format with several advanced features. To test the performance of the PMD, fine mapping of pea symbiotic genes Sym13 and Sym27 in linkage groups VII and V, respectively, was carried out. The results of mapping allowed us to propose the Sen1 gene (a homologue of SEN1 gene of Lotus japonicus (Regel) K. Larsen) as the best candidate gene for Sym13, and to narrow the list of possible candidate genes for Sym27 to ten, thus proving PMD to be useful for pea gene mapping and cloning. All information contained in PMD1 and PMD2 is available at www.peamarker.arriam.ru.
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Affiliation(s)
- Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Aleksandr I. Zhernakov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Alexey M. Afonin
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Sergei S. Boikov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
- Saint-Petersburg State University, Universitetskaya embankment, Saint-Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
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Jacobs A, Womack R, Chen M, Gharbi K, Elmer KR. Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes. Genetics 2017; 207:741-754. [PMID: 28760747 PMCID: PMC5629336 DOI: 10.1534/genetics.117.300093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/21/2017] [Indexed: 11/18/2022] Open
Abstract
The organization of functional regions within genomes has important implications for evolutionary potential. Considerable research effort has gone toward identifying the genomic basis of phenotypic traits of interest through quantitative trait loci (QTL) analyses. Less research has assessed the arrangement of QTL in the genome within and across species. To investigate the distribution, extent of colocalization, and the synteny of QTL for ecologically relevant traits, we used a comparative genomic mapping approach within and across a range of salmonid species. We compiled 943 QTL from all available species [lake whitefish (Coregonus clupeaformis), coho salmon (Oncorhynchus kisutch), rainbow trout (O. mykiss), Chinook salmon (O. tshawytscha), Atlantic salmon (Salmo salar), and Arctic charr (Salvelinus alpinus)]. We developed a novel analytical framework for mapping and testing the distribution of these QTL. We found no correlation between QTL density and gene density at the chromosome level but did at the fine-scale. Two chromosomes were significantly enriched for QTL. We found multiple synteny blocks for morphological, life history, and physiological traits across species, but only morphology and physiology had significantly more than expected. Two or three pairs of traits were significantly colocalized in three species (lake whitefish, coho salmon, and rainbow trout). Colocalization and fine-scale synteny suggest genetic linkage between traits within species and a conserved genetic basis across species. However, this pattern was weak overall, with colocalization and synteny being relatively rare. These findings advance our understanding of the role of genomic organization in the renowned ecological and phenotypic variability of salmonid fishes.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Robyn Womack
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Mel Chen
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, G12 8QQ, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3FL, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
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Liu R, Fang L, Yang T, Zhang X, Hu J, Zhang H, Han W, Hua Z, Hao J, Zong X. Marker-trait association analysis of frost tolerance of 672 worldwide pea (Pisum sativum L.) collections. Sci Rep 2017; 7:5919. [PMID: 28724947 PMCID: PMC5517424 DOI: 10.1038/s41598-017-06222-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/08/2017] [Indexed: 12/18/2022] Open
Abstract
Frost stress is one of the major abiotic stresses causing seedling death and yield reduction in winter pea. To improve the frost tolerance of pea, field evaluation of frost tolerance was conducted on 672 diverse pea accessions at three locations in Northern China in three growing seasons from 2013 to 2016 and marker-trait association analysis of frost tolerance were performed with 267 informative SSR markers in this study. Sixteen accessions were identified as the most winter-hardy for their ability to survive in all nine field experiments with a mean survival rate of 0.57, ranging from 0.41 to 0.75. Population structure analysis revealed a structured population of two sub-populations plus some admixtures in the 672 accessions. Association analysis detected seven markers that repeatedly had associations with frost tolerance in at least two different environments with two different statistical models. One of the markers is the functional marker EST1109 on LG VI which was predicted to co-localize with a gene involved in the metabolism of glycoproteins in response to chilling stress and may provide a novel mechanism of frost tolerance in pea. These winter-hardy germplasms and frost tolerance associated markers will play a vital role in marker-assisted breeding for winter-hardy pea cultivar.
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Affiliation(s)
- Rong Liu
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Fang
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tao Yang
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyan Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, Shandong, China
| | - Jinguo Hu
- USDA, Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164, USA
| | - Hongyan Zhang
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenliang Han
- Binzhou Academy of Agricultural Sciences, Binzhou, 256600, Shandong, China
| | - Zeke Hua
- Laiyang Agricultural Extension Center, Laiyang, 265200, Shandong, China
| | - Junjie Hao
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, Shandong, China
| | - Xuxiao Zong
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Molecular, Genetic and Agronomic Approaches to Utilizing Pulses as Cover Crops and Green Manure into Cropping Systems. Int J Mol Sci 2017; 18:ijms18061202. [PMID: 28587254 PMCID: PMC5486025 DOI: 10.3390/ijms18061202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/28/2017] [Accepted: 05/30/2017] [Indexed: 11/17/2022] Open
Abstract
Cover crops constitute one of the most promising agronomic practices towards a more sustainable agriculture. Their beneficial effects on main crops, soil and environment are many and various, while risks and disadvantages may also appear. Several legumes show a high potential but further research is required in order to suggest the optimal legume cover crops for each case in terms of their productivity and ability to suppress weeds. The additional cost associated with cover crops should also be addressed and in this context the use of grain legumes such as cowpea, faba bean and pea could be of high interest. Some of the aspects of these grain legumes as far as their use as cover crops, their genetic diversity and their breeding using conventional and molecular approaches are discussed in the present review. The specific species seem to have a high potential for use as cover crops, especially if their noticeable genetic diversity is exploited and their breeding focuses on several desirable traits.
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25
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Jha UC, Bohra A, Jha R. Breeding approaches and genomics technologies to increase crop yield under low-temperature stress. PLANT CELL REPORTS 2017; 36:1-35. [PMID: 27878342 DOI: 10.1007/s00299-016-2073-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/04/2016] [Indexed: 05/11/2023]
Abstract
Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research, Kanpur, 208024, India.
| | - Abhishek Bohra
- Indian Institute of Pulses Research, Kanpur, 208024, India.
| | - Rintu Jha
- Indian Institute of Pulses Research, Kanpur, 208024, India
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26
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Meziadi C, Blanchet S, Richard MMS, Pilet-Nayel ML, Geffroy V, Pflieger S. Bean pod mottle virus: a new powerful tool for functional genomics studies in Pisum sativum. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1777-87. [PMID: 26896301 PMCID: PMC5067550 DOI: 10.1111/pbi.12537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/13/2015] [Accepted: 01/06/2016] [Indexed: 05/08/2023]
Abstract
Pea (Pisum sativum L.) is an important legume worldwide. The importance of pea in arable rotations and nutritional value for both human and animal consumption have fostered sustained production and different studies to improve agronomic traits of interest. Moreover, complete sequencing of the pea genome is currently underway and will lead to the identification of a large number of genes potentially associated with important agronomic traits. Because stable genetic transformation is laborious for pea, virus-induced gene silencing (VIGS) appears as a powerful alternative technology for determining the function of unknown genes. In this work, we present a rapid and efficient viral inoculation method using DNA infectious plasmids of Bean pod mottle virus (BPMV)-derived VIGS vector. Six pea genotypes with important genes controlling biotic and/or abiotic stresses were found susceptible to BPMV carrying a GFP reporter gene and showed fluorescence in both shoots and roots. In a second step, we investigated 37 additional pea genotypes and found that 30 were susceptible to BPMV and only 7 were resistant. The capacity of BPMV to induce silencing of endogenes was investigated in the most susceptible genotype using two visual reporter genes: PsPDS and PsKORRIGAN1 (PsKOR1) encoding PHYTOENE DESATURASE and a 1,4-β-D-glucanase, respectively. The features of the 'one-step' BPMV-derived VIGS vector include (i) the ease of rub-inoculation, without any need for biolistic or agro-inoculation procedures, (ii) simple cost-effective procedure and (iii) noninterference of viral symptoms with silencing. These features make BPMV the most adapted VIGS vector in pea to make low- to high-throughput VIGS studies.
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Affiliation(s)
- Chouaib Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Sophie Blanchet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Manon M S Richard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | | | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
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27
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Guy E, Boulain H, Aigu Y, Le Pennec C, Chawki K, Morlière S, Schädel K, Kunert G, Simon JC, Sugio A. Optimization of Agroinfiltration in Pisum sativum Provides a New Tool for Studying the Salivary Protein Functions in the Pea Aphid Complex. FRONTIERS IN PLANT SCIENCE 2016; 7:1171. [PMID: 27555856 PMCID: PMC4977312 DOI: 10.3389/fpls.2016.01171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/20/2016] [Indexed: 05/06/2023]
Abstract
Aphids are piercing-sucking insect pests and feed on phloem sap. During feeding, aphids inject a battery of salivary proteins into host plant. Some of these proteins function like effectors of microbial pathogens and influence the outcome of plant-aphid interactions. The pea aphid (Acyrthosiphon pisum) is the model aphid and encompasses multiple biotypes each specialized to one or a few legume species, providing an opportunity to investigate the underlying mechanisms of the compatibility between plants and aphid biotypes. We aim to identify the aphid factors that determine the compatibility with host plants, hence involved in the host plant specialization process, and hypothesize that salivary proteins are one of those factors. Agrobacterium-mediated transient gene expression is a powerful tool to perform functional analyses of effector (salivary) proteins in plants. However, the tool was not established for the legume species that A. pisum feeds on. Thus, we decided to optimize the method for legume plants to facilitate the functional analyses of A. pisum salivary proteins. We screened a range of cultivars of pea (Pisum sativum) and alfalfa (Medicago sativa). None of the M. sativa cultivars was suitable for agroinfiltration under the tested conditions; however, we established a protocol for efficient transient gene expression in two cultivars of P. sativum, ZP1109 and ZP1130, using A. tumefaciens AGL-1 strain and the pEAQ-HT-DEST1 vector. We confirmed that the genes are expressed from 3 to 10 days post-infiltration and that aphid lines of the pea adapted biotype fed and reproduced on these two cultivars while lines of alfalfa and clover biotypes did not. Thus, the pea biotype recognizes these two cultivars as typical pea plants. By using a combination of ZP1109 and an A. pisum line, we defined an agroinfiltration procedure to examine the effect of in planta expression of selected salivary proteins on A. pisum fitness and demonstrated that transient expression of one candidate salivary gene increased the fecundity of the aphids. This result confirms that the agroinfiltration can be used to perform functional analyses of salivary proteins in P. sativum and consequently to study the molecular mechanisms underlying host specialization in the pea aphid complex.
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Affiliation(s)
- Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Yoann Aigu
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Charlotte Le Pennec
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Khaoula Chawki
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Kristina Schädel
- Department of Biochemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Grit Kunert
- Department of Biochemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant ProtectionLe Rheu, France
- *Correspondence: Akiko Sugio,
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28
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Tayeh N, Aluome C, Falque M, Jacquin F, Klein A, Chauveau A, Bérard A, Houtin H, Rond C, Kreplak J, Boucherot K, Martin C, Baranger A, Pilet-Nayel ML, Warkentin TD, Brunel D, Marget P, Le Paslier MC, Aubert G, Burstin J. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1257-73. [PMID: 26590015 DOI: 10.1111/tpj.13070] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/28/2015] [Accepted: 10/30/2015] [Indexed: 05/19/2023]
Abstract
Single nucleotide polymorphism (SNP) arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed and sustainable crop with a large (about 4.45 Gbp) but not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built providing insights into the structure and organization of the pea genome. Largely collinear genetic maps of 3918-8503 SNPs were obtained from all mapping populations, and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. A total of 12 802 transcript-derived SNP markers placed on a 15 079-marker high-density, high-resolution consensus map allowed the identification of ohnologue-rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further established, paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the structure and organization of the genome from this research will undoubtedly contribute to the understanding of the evolution of the pea genome and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for plant scientists to strengthen pea as a model for genetics and physiology and enhance breeding.
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Affiliation(s)
- Nadim Tayeh
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France
| | - Christelle Aluome
- INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France
| | - Matthieu Falque
- INRA, UMR320/UMR8120 Génétique Quantitative et Évolution - Le Moulon, F-91190, Gif-sur-Yvette, France
| | | | | | - Aurélie Chauveau
- INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France
| | - Aurélie Bérard
- INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France
| | - Hervé Houtin
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France
| | - Céline Rond
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France
| | | | | | | | - Alain Baranger
- INRA, UMR1349 Institut de Génétique Environnement et Protection des Plantes, F-35653, Le Rheu, France
| | - Marie-Laure Pilet-Nayel
- INRA, UMR1349 Institut de Génétique Environnement et Protection des Plantes, F-35653, Le Rheu, France
| | - Thomas D Warkentin
- Crop Development Centre, University of Saskatchewan, SK S7N 5A8, Saskatoon, Canada
| | - Dominique Brunel
- INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France
| | | | - Marie-Christine Le Paslier
- INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France
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29
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Tayeh N, Aubert G, Pilet-Nayel ML, Lejeune-Hénaut I, Warkentin TD, Burstin J. Genomic Tools in Pea Breeding Programs: Status and Perspectives. FRONTIERS IN PLANT SCIENCE 2015; 6:1037. [PMID: 26640470 PMCID: PMC4661580 DOI: 10.3389/fpls.2015.01037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/09/2015] [Indexed: 05/07/2023]
Abstract
Pea (Pisum sativum L.) is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22-25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome.
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Affiliation(s)
| | | | | | | | - Thomas D. Warkentin
- Crop Development Centre, College of Agriculture and Bioresources, University of SaskatchewanSaskatoon, SK, Canada
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Rameau C, Bertheloot J, Leduc N, Andrieu B, Foucher F, Sakr S. Multiple pathways regulate shoot branching. FRONTIERS IN PLANT SCIENCE 2015; 5:741. [PMID: 25628627 PMCID: PMC4292231 DOI: 10.3389/fpls.2014.00741] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/05/2014] [Indexed: 05/18/2023]
Abstract
Shoot branching patterns result from the spatio-temporal regulation of axillary bud outgrowth. Numerous endogenous, developmental and environmental factors are integrated at the bud and plant levels to determine numbers of growing shoots. Multiple pathways that converge to common integrators are most probably involved. We propose several pathways involving not only the classical hormones auxin, cytokinins and strigolactones, but also other signals with a strong influence on shoot branching such as gibberellins, sugars or molecular actors of plant phase transition. We also deal with recent findings about the molecular mechanisms and the pathway involved in the response to shade as an example of an environmental signal controlling branching. We propose the TEOSINTE BRANCHED1, CYCLOIDEA, PCF transcription factor TB1/BRC1 and the polar auxin transport stream in the stem as possible integrators of these pathways. We finally discuss how modeling can help to represent this highly dynamic system by articulating knowledges and hypothesis and calculating the phenotype properties they imply.
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Affiliation(s)
- Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
- Institut Jean-Pierre Bourgin, AgroParisTech, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | | | - Nathalie Leduc
- UMR1345 IRHS, Université d’Angers, SFR 4207 QUASAV, Angers, France
| | - Bruno Andrieu
- UMR1091 EGC, INRA, Thiverval-Grignon, France
- UMR1091 EGC, AgroParisTech, Thiverval-Grignon, France
| | | | - Soulaiman Sakr
- UMR1345 IRHS, Agrocampus-Ouest, SFR 4207 QUASAV, Angers, France
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Weller JL, Ortega R. Genetic control of flowering time in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:207. [PMID: 25914700 PMCID: PMC4391241 DOI: 10.3389/fpls.2015.00207] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/15/2015] [Indexed: 05/18/2023]
Abstract
The timing of flowering, and in particular the degree to which it is responsive to the environment, is a key factor in the adaptation of a given species to various eco-geographic locations and agricultural practices. Flowering time variation has been documented in many crop legumes, and selection for specific variants has permitted significant expansion and improvement in cultivation, from prehistoric times to the present day. Recent advances in legume genomics have accelerated the process of gene identification and functional analysis, and opened up new prospects for a molecular understanding of flowering time adaptation in this important crop group. Within the legumes, two species have been prominent in flowering time studies; the vernalization-responsive long-day species pea (Pisum sativum) and the warm-season short-day plant soybean (Glycine max). Analysis of flowering in these species is now being complemented by reverse genetics capabilities in the model legumes Medicago truncatula and Lotus japonicus, and the emergence of genome-scale resources in a range of other legumes. This review will outline the insights gained from detailed forward genetic analysis of flowering time in pea and soybean, highlighting the importance of light perception, the circadian clock and the FT family of flowering integrators. It discusses the current state of knowledge on genetic mechanisms for photoperiod and vernalization response, and concludes with a broader discussion of flowering time adaptation across legumes generally.
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Affiliation(s)
- James L. Weller
- *Correspondence: James L. Weller, School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
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Sindhu A, Ramsay L, Sanderson LA, Stonehouse R, Li R, Condie J, Shunmugam ASK, Liu Y, Jha AB, Diapari M, Burstin J, Aubert G, Tar’an B, Bett KE, Warkentin TD, Sharpe AG. Gene-based SNP discovery and genetic mapping in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2225-41. [PMID: 25119872 PMCID: PMC4180032 DOI: 10.1007/s00122-014-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 07/29/2014] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Pea (Pisum sativum L.) is one of the world's oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.
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Affiliation(s)
- Anoop Sindhu
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Larissa Ramsay
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
- Present Address: Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Lacey-Anne Sanderson
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Robert Stonehouse
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Rong Li
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Janet Condie
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Arun S. K. Shunmugam
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Yong Liu
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Ambuj B. Jha
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Marwan Diapari
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Judith Burstin
- UMR1347 Agroecology, INRA, 17 rue de Sully, 21065 Dijon Cedex, France
| | - Gregoire Aubert
- UMR1347 Agroecology, INRA, 17 rue de Sully, 21065 Dijon Cedex, France
| | - Bunyamin Tar’an
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Kirstin E. Bett
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Thomas D. Warkentin
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Andrew G. Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
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Baldwin L, Domon JM, Klimek JF, Fournet F, Sellier H, Gillet F, Pelloux J, Lejeune-Hénaut I, Carpita NC, Rayon C. Structural alteration of cell wall pectins accompanies pea development in response to cold. PHYTOCHEMISTRY 2014; 104:37-47. [PMID: 24837358 DOI: 10.1016/j.phytochem.2014.04.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 04/11/2014] [Accepted: 04/14/2014] [Indexed: 05/23/2023]
Abstract
Pea (Pisum sativum) cell wall metabolism in response to chilling was investigated in a frost-sensitive genotype 'Terese' and a frost-tolerant genotype 'Champagne'. Cell walls isolated from stipules of cold acclimated and non-acclimated plants showed that cold temperatures induce changes in polymers containing xylose, arabinose, galactose and galacturonic acid residues. In the tolerant cultivar Champagne, acclimation is accompanied by increases in homogalacturonan, xylogalacturonan and highly branched Rhamnogalacturonan I with branched and unbranched (1→5)-α-arabinans and (1→4)-β-galactans. In contrast, the sensitive cultivar Terese accumulates substantial amounts of (1→4)-β-xylans and glucuronoxylan, but not the pectins. Greater JIM7 labeling was observed in Champagne compared to Terese, indicating that cold acclimation also induces an increase in the degree of methylesterification of pectins. Significant decrease in polygalacturonase activities in both genotypes were observed at the end of cold acclimation. These data indicate a role for esterified pectins in cold tolerance. The possible functions for pectins and their associated arabinans and galactans in cold acclimation are discussed.
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Affiliation(s)
- Laëtitia Baldwin
- EA 3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Jean-Marc Domon
- EA 3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - John F Klimek
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, United States.
| | - Françoise Fournet
- EA 3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Hélène Sellier
- INRA USTL UMR 1281, Laboratoire de Génétique et d'Amélioration des Plantes, Estrées-Mons BP50136, 80203 Péronne, France.
| | - Françoise Gillet
- EA 3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Jérôme Pelloux
- EA 3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Isabelle Lejeune-Hénaut
- INRA USTL UMR 1281, Laboratoire de Génétique et d'Amélioration des Plantes, Estrées-Mons BP50136, 80203 Péronne, France.
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, United States.
| | - Catherine Rayon
- EA 3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
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Klein A, Houtin H, Rond C, Marget P, Jacquin F, Boucherot K, Huart M, Rivière N, Boutet G, Lejeune-Hénaut I, Burstin J. QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1319-30. [PMID: 24695842 DOI: 10.1007/s00122-014-2299-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/12/2014] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE Avoidance mechanisms and intrinsic resistance are complementary strategies to improve winter frost tolerance and yield potential in field pea. The development of the winter pea crop represents a major challenge to expand plant protein production in temperate areas. Breeding winter cultivars requires the combination of freezing tolerance as well as high seed productivity and quality. In this context, we investigated the genetic determinism of winter frost tolerance and assessed its genetic relationship with yield and developmental traits. Using a newly identified source of frost resistance, we developed a population of recombinant inbred lines and evaluated it in six environments in Dijon and Clermont-Ferrand between 2005 and 2010. We developed a genetic map comprising 679 markers distributed over seven linkage groups and covering 947.1 cM. One hundred sixty-one quantitative trait loci (QTL) explaining 9-71 % of the phenotypic variation were detected across the six environments for all traits measured. Two clusters of QTL mapped on the linkage groups III and one cluster on LGVI reveal the genetic links between phenology, morphology, yield-related traits and frost tolerance in winter pea. QTL clusters on LGIII highlighted major developmental gene loci (Hr and Le) and the QTL cluster on LGVI explained up to 71 % of the winter frost damage variation. This suggests that a specific architecture and flowering ideotype defines frost tolerance in winter pea. However, two consistent frost tolerance QTL on LGV were independent of phenology and morphology traits, showing that different protective mechanisms are involved in frost tolerance. Finally, these results suggest that frost tolerance can be bred independently to seed productivity and quality.
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Affiliation(s)
- Anthony Klein
- INRA, UMR 1347 Agroécologie, BP 86510, 21000, Dijon Cedex, France,
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Henson CA, Duke SH, Livingston DP. Metabolic changes in Avena sativa crowns recovering from freezing. PLoS One 2014; 9:e93085. [PMID: 24675792 PMCID: PMC3968094 DOI: 10.1371/journal.pone.0093085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/01/2014] [Indexed: 12/03/2022] Open
Abstract
Extensive research has been conducted on cold acclimation and freezing tolerance of fall-sown cereal plants due to their economic importance; however, little has been reported on the biochemical changes occurring over time after the freezing conditions are replaced by conditions favorable for recovery and growth such as would occur during spring. In this study, GC-MS was used to detect metabolic changes in the overwintering crown tissue of oat (Avena sativa L.) during a fourteen day time-course after freezing. Metabolomic analysis revealed increases in most amino acids, particularly proline, 5-oxoproline and arginine, which increased greatly in crowns that were frozen compared to controls and correlated very significantly with days after freezing. In contrast, sugar and sugar related metabolites were little changed by freezing, except sucrose and fructose which decreased dramatically. In frozen tissue all TCA cycle metabolites, especially citrate and malate, decreased in relation to unfrozen tissue. Alterations in some amino acid pools after freezing were similar to those observed in cold acclimation whereas most changes in sugar pools after freezing were not. These similarities and differences suggest that there are common as well as unique genetic mechanisms between these two environmental conditions that are crucial to the winter survival of plants.
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Affiliation(s)
- Cynthia A. Henson
- United States Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Madison, Wisconsin, United States of America
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Stanley H. Duke
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - David P. Livingston
- United States Department of Agriculture-Agricultural Research Service and Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
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Duarte J, Rivière N, Baranger A, Aubert G, Burstin J, Cornet L, Lavaud C, Lejeune-Hénaut I, Martinant JP, Pichon JP, Pilet-Nayel ML, Boutet G. Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea. BMC Genomics 2014; 15:126. [PMID: 24521263 PMCID: PMC3925251 DOI: 10.1186/1471-2164-15-126] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 02/05/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis. RESULTS We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs.We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species. CONCLUSIONS Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding.
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Affiliation(s)
- Jorge Duarte
- Biogemma, route d’Ennezat, CS 90126, Chappes 63720, France
| | | | - Alain Baranger
- INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France
| | - Grégoire Aubert
- INRA UMR 1347 Agroécologie, Bat. Mendel, 17 rue Sully BP 86510, Dijon 21065, France
| | - Judith Burstin
- INRA UMR 1347 Agroécologie, Bat. Mendel, 17 rue Sully BP 86510, Dijon 21065, France
| | - Laurent Cornet
- Biogemma, route d’Ennezat, CS 90126, Chappes 63720, France
| | - Clément Lavaud
- INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France
| | | | - Jean-Pierre Martinant
- Limagrain Europe, centre de recherche route d’Ennezat, CS 3911, Chappes 63720, France
| | | | | | - Gilles Boutet
- INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France
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Legrand S, Marque G, Blassiau C, Bluteau A, Canoy AS, Fontaine V, Jaminon O, Bahrman N, Mautord J, Morin J, Petit A, Baranger A, Rivière N, Wilmer J, Delbreil B, Lejeune-Hénaut I. Combining gene expression and genetic analyses to identify candidate genes involved in cold responses in pea. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1148-57. [PMID: 23632303 DOI: 10.1016/j.jplph.2013.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 06/02/2023]
Abstract
Cold stress affects plant growth and development. In order to better understand the responses to cold (chilling or freezing tolerance), we used two contrasted pea lines. Following a chilling period, the Champagne line becomes tolerant to frost whereas the Terese line remains sensitive. Four suppression subtractive hybridisation libraries were obtained using mRNAs isolated from pea genotypes Champagne and Terese. Using quantitative polymerase chain reaction (qPCR) performed on 159 genes, 43 and 54 genes were identified as differentially expressed at the initial time point and during the time course study, respectively. Molecular markers were developed from the differentially expressed genes and were genotyped on a population of 164 RILs derived from a cross between Champagne and Terese. We identified 5 candidate genes colocalizing with 3 different frost damage quantitative trait loci (QTL) intervals and a protein quantity locus (PQL) rich region previously reported. This investigation revealed the role of constitutive differences between both genotypes in the cold responses, in particular with genes related to glycine degradation pathway that could confer to Champagne a better frost tolerance. We showed that freezing tolerance involves a decrease of expression of genes related to photosynthesis and the expression of a gene involved in the production of cysteine and methionine that could act as cryoprotectant molecules. Although it remains to be confirmed, this study could also reveal the involvement of the jasmonate pathway in the cold responses, since we observed that two genes related to this pathway were mapped in a frost damage QTL interval and in a PQL rich region interval, respectively.
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Affiliation(s)
- Sylvain Legrand
- Université Lille 1, UMR SADV 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, Université Lille Nord de France, Lille 1, SN2, F-59650 Villeneuve d'Ascq, France.
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Avia K, Pilet-Nayel ML, Bahrman N, Baranger A, Delbreil B, Fontaine V, Hamon C, Hanocq E, Niarquin M, Sellier H, Vuylsteker C, Prosperi JM, Lejeune-Hénaut I. Genetic variability and QTL mapping of freezing tolerance and related traits in Medicago truncatula. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2353-66. [PMID: 23778689 DOI: 10.1007/s00122-013-2140-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 06/01/2013] [Indexed: 05/10/2023]
Abstract
Freezing is a major environmental limitation to crop productivity for a number of species including legumes. We investigated the genetic determinism of freezing tolerance in the model legume Medicago truncatula Gaertn (M. truncatula). After having observed a large variation for freezing tolerance among 15 M. truncatula accessions, the progeny of a F6 recombinant inbred line population, derived from a cross between two accessions, was acclimated to low above-freezing temperatures and assessed for: (a) number of leaves (NOL), leaf area (LA), chlorophyll content index (CCI), shoot and root dry weights (SDW and RDW) at the end of the acclimation period and (b) visual freezing damage (FD) during the freezing treatment and 2 weeks after regrowth and foliar electrolyte leakage (EL) 2 weeks after regrowth. Consistent QTL positions with additive effects for FD were found on LG1, LG4 and LG6, the latter being the most explanatory (R (2) ≈ 40 %). QTL for NOL, QTL for EL, NOL and RDW, and QTL for EL and CCI colocalized with FD QTL on LG1, LG4 and LG6, respectively. Favorable alleles for these additive effects were brought by the same parent suggesting that this accession contributes to superior freezing tolerance by affecting plants' capacity to maintain growth at low above-freezing temperatures. No epistatic effects were found between FD QTL, but for each of the studied traits, 3-6 epistatic effects were detected between loci not detected directly as QTL. These results open the way to the assessment of syntenic relationships between QTL for frost tolerance in M. truncatula and cultivated legume species.
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Affiliation(s)
- Komlan Avia
- Institut National de la Recherche Agronomique, UMR 1281 SADV, Estrées-Mons, Péronne Cedex, France
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Hamon C, Coyne CJ, McGee RJ, Lesné A, Esnault R, Mangin P, Hervé M, Le Goff I, Deniot G, Roux-Duparque M, Morin G, McPhee KE, Delourme R, Baranger A, Pilet-Nayel ML. QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea. BMC PLANT BIOLOGY 2013; 13:45. [PMID: 23497245 PMCID: PMC3680057 DOI: 10.1186/1471-2229-13-45] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/04/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND Development of durable plant genetic resistance to pathogens through strategies of QTL pyramiding and diversification requires in depth knowledge of polygenic resistance within the available germplasm. Polygenic partial resistance to Aphanomyces root rot, caused by Aphanomyces euteiches, one of the most damaging pathogens of pea worldwide, was previously dissected in individual mapping populations. However, there are no data available regarding the diversity of the resistance QTL across a broader collection of pea germplasm. In this study, we performed a meta-analysis of Aphanomyces root rot resistance QTL in the four main sources of resistance in pea and compared their genomic localization with genes/QTL controlling morphological or phenological traits and with putative candidate genes. RESULTS Meta-analysis, conducted using 244 individual QTL reported previously in three mapping populations (Puget x 90-2079, Baccara x PI180693 and Baccara x 552) and in a fourth mapping population in this study (DSP x 90-2131), resulted in the identification of 27 meta-QTL for resistance to A. euteiches. Confidence intervals of meta-QTL were, on average, reduced four-fold compared to mean confidence intervals of individual QTL. Eleven consistent meta-QTL, which highlight seven highly consistent genomic regions, were identified. Few meta-QTL specificities were observed among mapping populations, suggesting that sources of resistance are not independent. Seven resistance meta-QTL, including six of the highly consistent genomic regions, co-localized with six of the meta-QTL identified in this study for earliness and plant height and with three morphological genes (Af, A, R). Alleles contributing to the resistance were often associated with undesirable alleles for dry pea breeding. Candidate genes underlying six main meta-QTL regions were identified using colinearity between the pea and Medicago truncatula genomes. CONCLUSIONS QTL meta-analysis provided an overview of the moderately low diversity of loci controlling partial resistance to A. euteiches in four main sources of resistance in pea. Seven highly consistent genomic regions with potential use in marker-assisted-selection were identified. Confidence intervals at several main QTL regions were reduced and co-segregation among resistance and morphological/phenological alleles was identified. Further work will be required to identify the best combinations of QTL for durably increasing partial resistance to A. euteiches.
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Affiliation(s)
- Céline Hamon
- INRA, UMR1349 IGEPP, Le Rheu F-35653, France
- Current address: Vegenov-BBV, Penn ar Prat, Saint Pol de Léon, 29250, France
| | - Clarice J Coyne
- USDA, ARS, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164-6402, USA
| | - Rebecca J McGee
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA, 99164-6434, USA
| | | | | | - Pierre Mangin
- INRA, Domaine Expérimental d’Epoisses, UE0115, Bretenières, F-21110, France
| | - Marie Hervé
- INRA, UMR1349 IGEPP, Le Rheu F-35653, France
- Current address: HM CLAUSE, 1 chemin ronzières, La Bohalle, 49800, France
| | - Isabelle Le Goff
- INRA, UMR1349 IGEPP, Le Rheu F-35653, France
- Current address: INRA, UMR1301 IBSV Interactions Biotiques en Santé Végétale, 400 route des Chappes, Sophia Antipolis Cedex, 06903, France
| | | | - Martine Roux-Duparque
- GSP, Domaine Brunehaut, Estrées-Mons, 80200, France
- Current address: Chambre d'Agriculture de l'Aisne, 1 rue René Blondelle, Laon Cedex, 02007, France
| | | | - Kevin E McPhee
- Department 7670, North Dakota State University, 370G Loftsgard Hall, Fargo, ND, 58108-6050, USA
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Weller JL, Hecht VFG, Sussmilch FC. Isolation and forward genetic analysis of developmental genes in pea. Methods Mol Biol 2013; 1069:147-61. [PMID: 23996314 DOI: 10.1007/978-1-62703-613-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding of developmental processes relies heavily on isolation and functional characterization of relevant genes. The garden pea (Pisum sativum L.) is one of the classic model species in plant genetics and has been used for a wide range of physiological and molecular studies of plant development. Here we describe the resources and approaches available for isolation of genes and genetic characterization of loci affecting development in pea.
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Affiliation(s)
- James L Weller
- School of Plant Science, University of Tasmania, Hobart, TAS, Australia
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41
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Weller JL, Liew LC, Hecht VFG, Rajandran V, Laurie RE, Ridge S, Wenden B, Vander Schoor JK, Jaminon O, Blassiau C, Dalmais M, Rameau C, Bendahmane A, Macknight RC, Lejeune-Hénaut I. A conserved molecular basis for photoperiod adaptation in two temperate legumes. Proc Natl Acad Sci U S A 2012; 109:21158-63. [PMID: 23213200 PMCID: PMC3529011 DOI: 10.1073/pnas.1207943110] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Legumes were among the first plant species to be domesticated, and accompanied cereals in expansion of agriculture from the Fertile Crescent into diverse environments across the Mediterranean basin, Europe, Central Asia, and the Indian subcontinent. Although several recent studies have outlined the molecular basis for domestication and eco-geographic adaptation in the two main cereals from this region, wheat and barley, similar questions remain largely unexplored in their legume counterparts. Here we identify two major loci controlling differences in photoperiod response between wild and domesticated pea, and show that one of these, high response to photoperiod (HR), is an ortholog of early flowering 3 (ELF3), a gene involved in circadian clock function. We found that a significant proportion of flowering time variation in global pea germplasm is controlled by HR, with a single, widespread functional variant conferring altered circadian rhythms and the reduced photoperiod response associated with the spring habit. We also present evidence that ELF3 has a similar role in lentil, another major legume crop, with a distinct functional variant contributing to reduced photoperiod response in cultivars widely deployed in short-season environments. Our results identify the factor likely to have permitted the successful prehistoric expansion of legume cultivation to Northern Europe, and define a conserved genetic basis for major adaptive changes in flowering phenology and growth habit in an important crop group.
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Affiliation(s)
- James L Weller
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia.
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Le May C, Guibert M, Leclerc A, Andrivon D, Tivoli B. A single, plastic population of Mycosphaerella pinodes causes ascochyta blight on winter and spring peas (Pisum sativum) in France. Appl Environ Microbiol 2012; 78:8431-40. [PMID: 23023742 PMCID: PMC3497390 DOI: 10.1128/aem.01543-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/19/2012] [Indexed: 11/20/2022] Open
Abstract
Plant diseases are caused by pathogen populations continuously subjected to evolutionary forces (genetic flow, selection, and recombination). Ascochyta blight, caused by Mycosphaerella pinodes, is one of the most damaging necrotrophic pathogens of field peas worldwide. In France, both winter and spring peas are cultivated. Although these crops overlap by about 4 months (March to June), primary Ascochyta blight infections are not synchronous on the two crops. This suggests that the disease could be due to two different M. pinodes populations, specialized on either winter or spring pea. To test this hypothesis, 144 pathogen isolates were collected in the field during the winter and spring growing seasons in Rennes (western France), and all the isolates were genotyped using amplified fragment length polymorphism (AFLP) markers. Furthermore, the pathogenicities of 33 isolates randomly chosen within the collection were tested on four pea genotypes (2 winter and 2 spring types) grown under three climatic regimes, simulating winter, late winter, and spring conditions. M. pinodes isolates from winter and spring peas were genetically polymorphic but not differentiated according to the type of cultivars. Isolates from winter pea were more pathogenic than isolates from spring pea on hosts raised under winter conditions, while isolates from spring pea were more pathogenic than those from winter pea on plants raised under spring conditions. These results show that disease developed on winter and spring peas was initiated by a single population of M. pinodes whose pathogenicity is a plastic trait modulated by the physiological status of the host plant.
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Lucau-Danila A, Toitot C, Goulas E, Blervacq AS, Hot D, Bahrman N, Sellier H, Lejeune-Hénaut I, Delbreil B. Transcriptome analysis in pea allows to distinguish chilling and acclimation mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 58:236-44. [PMID: 22858528 DOI: 10.1016/j.plaphy.2012.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/12/2012] [Indexed: 05/04/2023]
Abstract
In order to distinguish chilling and freezing tolerance mechanisms in pea, responses to cold exposure were compared between the freezing tolerant line Champagne and the sensitive line Terese. Global gene expression was considered in the two lines and associated with morphological, histological and biochemical approaches. The chilling tolerance in both lines was related to responses of the CBF, COR and LEA genes belonging to the CBF regulon, with greater earliness of expression in the Champagne genotype. The freezing tolerance, only observed in Champagne, was associated with acclimation processes such as cellular osmotic stabilization, photosynthesis modifications, antioxidants production, modifications in hormone metabolism, cell wall composition and dynamics.
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Affiliation(s)
- A Lucau-Danila
- UMR 1281, Université Lille1-INRA, USTL, Stress Abiotiques et Différenciation des Végétaux cultivés, Bâtiment SN2, F-59650 Villeneuve d'Ascq, France.
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Hamon C, Baranger A, Coyne CJ, McGee RJ, Le Goff I, L'anthoëne V, Esnault R, Rivière JP, Klein A, Mangin P, McPhee KE, Roux-Duparque M, Porter L, Miteul H, Lesné A, Morin G, Onfroy C, Moussart A, Tivoli B, Delourme R, Pilet-Nayel ML. New consistent QTL in pea associated with partial resistance to Aphanomyces euteiches in multiple French and American environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:261-81. [PMID: 21479935 DOI: 10.1007/s00122-011-1582-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Accepted: 03/23/2011] [Indexed: 05/03/2023]
Abstract
Partial resistances, often controlled by quantitative trait loci (QTL), are considered to be more durable than monogenic resistances. Therefore, a precursor to developing efficient breeding programs for polygenic resistance to pathogens should be a greater understanding of genetic diversity and stability of resistance QTL in plants. In this study, we deciphered the diversity and stability of resistance QTL to Aphanomyces euteiches in pea towards pathogen variability, environments and scoring criteria, from two new sources of partial resistance (PI 180693 and 552), effective in French and USA infested fields. Two mapping populations of 178 recombinant inbred lines each, derived from crosses between 552 or PI 180693 (partially resistant) and Baccara (susceptible), were used to identify QTL for Aphanomyces root rot resistance in controlled and in multiple French and USA field conditions using several resistance criteria. We identified a total of 135 additive-effect QTL corresponding to 23 genomic regions and 13 significant epistatic interactions associated with partial resistance to A. euteiches in pea. Among the 23 additive-effect genomic regions identified, five were consistently detected, and showed highly stable effects towards A. euteiches strains, environments, resistance criteria, condition tests and RIL populations studied. These results confirm the complexity of inheritance of partial resistance to A. euteiches in pea and provide good bases for the choice of consistent QTL to use in marker-assisted selection schemes to increase current levels of resistance to A. euteiches in pea breeding programs.
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Affiliation(s)
- Céline Hamon
- Université de Rennes 1, Amélioration des Plantes et Biotechnologies Végétales, Rennes, France.
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46
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Gery C, Zuther E, Schulz E, Legoupi J, Chauveau A, McKhann H, Hincha DK, Téoulé E. Natural variation in the freezing tolerance of Arabidopsis thaliana: effects of RNAi-induced CBF depletion and QTL localisation vary among accessions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:12-23. [PMID: 21421342 DOI: 10.1016/j.plantsci.2010.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 07/13/2010] [Accepted: 07/17/2010] [Indexed: 05/20/2023]
Abstract
Plants from temperate regions are able to withstand freezing temperatures and to increase their freezing tolerance during exposure to low, but non-freezing, temperatures through a process known as cold acclimation. Key regulatory proteins in this process are the cold-induced CBF1, 2 and 3 transcription factors which control many cold regulated genes. Although much work has focused on this signal transduction pathway, the details of its regulation and of its quantitative contribution to cold acclimation are still unclear. Here, we have used the large natural variation present in the 48 accessions of the Versailles core collection of Arabidopsis thaliana to further elucidate the function of the CBF transcription factors. CBF gene expression studies showed that the freezing sensitive accessions had mostly low expression levels 2h after transfer of plants to 5°C, while the most tolerant accessions showed a wide range of CBF expression levels. To investigate the quantitative contribution of CBF expression to plant freezing tolerance and low temperature growth performance, RNAi lines targeting all three CBF genes were produced in eight different accessions. We observed striking differences between different accessions in the effects that reduced CBF expression had on freezing tolerance, while effects on growth were generally too small to draw firm conclusions. Analysis of CBF expression indicated a tight co-regulation between CBF1 and CBF3, while the relationship between the expression levels of CBF2 and CBF1 or CBF3 strongly depended on the genetic background of the RNAi lines. In agreement with the observed differences between the different accessions, QTL analyses with two different RIL populations indicated that QTL localisation varies strongly between populations. Collectively, these results show that both the regulation of the CBF genes and their relative contribution to freezing tolerance strongly depend on the accession studied. In addition, natural variation is suggested to be an interesting source of novel regulatory pathways and genes that may be useful in the future for improving plant freezing tolerance.
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Affiliation(s)
- Carine Gery
- Institut Jean-Pierre Bourgin (IJPB), UMR1318 INRA-AgroParisTech, Bât. 7, INRA Centre de Versailles-Grignon, Route de Saint Cyr, 78026 Versailles Cedex, France
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Deulvot C, Charrel H, Marty A, Jacquin F, Donnadieu C, Lejeune-Hénaut I, Burstin J, Aubert G. Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea. BMC Genomics 2010; 11:468. [PMID: 20701750 PMCID: PMC3091664 DOI: 10.1186/1471-2164-11-468] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 08/11/2010] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. RESULTS We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. CONCLUSION Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.
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Affiliation(s)
| | | | - Amandine Marty
- GENOTOUL Platform, INRA chemin de Borde-Rouge BP52627 31326 Auzeville, France
- Euralis semences, Domaine de Sandreau, 31700 Mondonville, France
| | | | - Cécile Donnadieu
- GENOTOUL Platform, INRA chemin de Borde-Rouge BP52627 31326 Auzeville, France
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Bourion V, Rizvi SMH, Fournier S, de Larambergue H, Galmiche F, Marget P, Duc G, Burstin J. Genetic dissection of nitrogen nutrition in pea through a QTL approach of root, nodule, and shoot variability. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:71-86. [PMID: 20180092 DOI: 10.1007/s00122-010-1292-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/28/2010] [Indexed: 05/03/2023]
Abstract
Pea (Pisum sativum L.) is the third most important grain legume worldwide, and the increasing demand for protein-rich raw material has led to a great interest in this crop as a protein source. Seed yield and protein content in crops are strongly determined by nitrogen (N) nutrition, which in legumes relies on two complementary pathways: absorption by roots of soil mineral nitrogen, and fixation in nodules of atmospheric dinitrogen through the plant-Rhizobium symbiosis. This study assessed the potential of naturally occurring genetic variability of nodulated root structure and functioning traits to improve N nutrition in pea. Glasshouse and field experiments were performed on seven pea genotypes and on the 'Cameor' x 'Ballet' population of recombinant inbred lines selected on the basis of parental contrast for root and nodule traits. Significant variation was observed for most traits, which were obtained from non-destructive kinetic measurements of nodulated root and shoot in pouches, root and shoot image analysis, (15)N quantification, or seed yield and protein content determination. A significant positive relationship was found between nodule establishment and root system growth, both among the seven genotypes and the RIL population. Moreover, several quantitative trait loci for root or nodule traits and seed N accumulation were mapped in similar locations, highlighting the possibility of breeding new pea cultivars with increased root system size, sustained nodule number, and improved N nutrition. The impact on both root or nodule traits and N nutrition of the genomic regions of the major developmental genes Le and Af was also underlined.
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Affiliation(s)
- Virginie Bourion
- INRA, UMR102, Genetics and Ecophysiology of Grain Legumes, BP 86510, 21065, Dijon, France.
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Abstract
As part of a breeding strategy applied to pea (Pisum sativum L.), we propose the use of modelling as a tool for studying flowering time. The pea, both a crop and a model species for developmental processes, represents a valuable tool for systems biology approaches. A preliminary computational model for flowering control was previously developed based on genetic and physiological approaches. This paper discusses possible improvements of the model based on recent molecular advances on the regulation of flowering in peas and the model species Arabidopsis thaliana. A combination of a genetic approach together with agroecophysiological models that are not based on genotype, built into a complete model for flowering time prediction is also proposed. This complete model should allow an accurate prediction of flower initiation and also provide an integrative tool that will be useful for various purposes, from genetic networks to crop models.
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Affiliation(s)
- Bénédicte Wenden
- INRA, Institut JP Bourgin, UR 254 station de génétique et d'amélioration des plantes, 78026 Versailles, France.
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Liew LC, Hecht V, Laurie RE, Knowles CL, Vander Schoor JK, Macknight RC, Weller JL. DIE NEUTRALIS and LATE BLOOMER 1 contribute to regulation of the pea circadian clock. THE PLANT CELL 2009; 21:3198-211. [PMID: 19843842 PMCID: PMC2782296 DOI: 10.1105/tpc.109.067223] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 09/09/2009] [Accepted: 09/25/2009] [Indexed: 05/18/2023]
Abstract
The DIE NEUTRALIS (DNE) locus in garden pea (Pisum sativum) was previously shown to inhibit flowering under noninductive short-day conditions and to affect a graft-transmissible flowering signal. In this study, we establish that DNE has a role in diurnal and/or circadian regulation of several clock genes, including the pea GIGANTEA (GI) ortholog LATE BLOOMER 1 (LATE1) and orthologs of the Arabidopsis thaliana genes LATE ELONGATED HYPOCOTYL and TIMING OF CHLOROPHYLL A/B BINDING PROTEIN EXPRESSION 1. We also confirm that LATE1 participates in the clock and provide evidence that DNE is the ortholog of Arabidopsis EARLY FLOWERING4 (ELF4). Circadian rhythms of clock gene expression in wild-type plants under constant light were weaker in pea than in Arabidopsis, and a number of differences were also seen in the effects of both DNE/ELF4 and LATE1/GI on clock gene expression. Grafting studies suggest that DNE controls flowering at least in part through a LATE1-dependent mobile stimulus, and dne mutants show elevated expression of a FLOWERING LOCUS T homolog under short-day conditions. However, the early flowering of the dne mutant is not associated with altered expression of a previously described CONSTANS-like gene. Collectively, our results characterize the clock system and reveal its importance for photoperiod responsiveness in a model legume.
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Affiliation(s)
- Lim Chee Liew
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Valérie Hecht
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Rebecca E. Laurie
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Claire L. Knowles
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia
| | | | | | - James L. Weller
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia
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